R: Manipulate 'EpiTrax' Data and Generate Reports

# Manipulate 'EpiTrax' Data and Generate Reports

## Documentation for package ‘epitraxr’ version 0.5.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

clear_old_reports | Clear out old reports before generating new ones.
compute_trend | Compute the report trend
convert_counts_to_rate | Convert case counts to rate
create_epitrax_from_file | Create an EpiTrax object from data file
create_filesystem | Create filesystem
create_public_report_combined_month_ytd | Create combined monthly and year-to-date public report
create_public_report_month | Create a monthly cross-section public report
create_public_report_ytd | Create a YTD public report
create_report_annual_counts | Create annual counts report
create_report_grouped_stats | Create grouped disease statistics report
create_report_monthly_avgs | Create monthly averages report
create_report_monthly_counts | Create monthly counts report
create_report_monthly_medians | Create monthly medians report
create_report_ytd_counts | Create year-to-date (YTD) counts report
create_report_ytd_medians | Create year-to-date (YTD) medians report
epitraxr_config | Create epitraxr config object
epitrax_ireport_annual_counts | Create annual counts internal report from an EpiTrax object
epitrax_ireport_monthly_avgs | Create monthly averages internal report from an EpiTrax object
epitrax_ireport_monthly_counts_all_yrs | Create monthly counts internal report for all years from an EpiTrax object
epitrax_ireport_ytd_counts_for_month | Create year-to-date (YTD) counts internal report for a given month from an EpiTrax object
epitrax_preport_combined_month_ytd | Create combined monthly/YTD stats public report from an EpiTrax object
epitrax_preport_month_crosssections | Create monthly cross-section reports from an EpiTrax object
epitrax_preport_ytd_rates | Create year-to-date (YTD) rates public report from an EpiTrax object
epitrax_report_grouped_stats | Create grouped disease statistics report from an EpiTrax object
epitrax_report_monthly_medians | Create monthly medians report from an EpiTrax object
epitrax_report_ytd_medians | Create year-to-date (YTD) medians report from an EpiTrax object
epitrax_set_config_from_file | Set report configuration of EpiTrax object from config file
epitrax_set_config_from_list | Set report configuration of EpiTrax object from list
epitrax_set_report_diseases | Set report diseases in EpiTrax object
epitrax_write_csvs | Write reports from EpiTrax object to CSV files
epitrax_write_pdf_grouped_stats | Write grouped statistics reports from EpiTrax object to PDF files
epitrax_write_pdf_public_reports | Create formatted PDF report of monthly cross-section reports
epitrax_write_xlsxs | Write reports from EpiTrax object to Excel files
format_epitrax_data | Format EpiTrax data for report generation
get_month_counts | Get monthly counts for each disease
get_report_config | Read in the report config YAML file
get_report_diseases | Get both internal and public disease lists
get_report_diseases_internal | Get the internal disease list
get_report_diseases_public | Get the public disease list
get_yrs | Get unique years from the data
mmwr_week_to_month | Convert MMWR week to calendar month
read_epitrax_data | Read in EpiTrax data
reshape_annual_wide | Reshape data with each year as a separate column
reshape_monthly_wide | Reshape data with each month as a separate column
run_app | Launch the epitraxr Shiny Application
setup_epitrax | Setup EpiTrax object with configuration and disease lists
setup_filesystem | Setup the report filesystem
set_na_0 | Set NA values to 0
standardize_report_diseases | Standardize diseases for report
validate_config | Validate config
validate_data | Validate input EpiTrax data
validate_epitrax | Validate EpiTrax object
validate_filesystem | Validate filesystem structure
write_report_csv | Write report CSV files
write_report_pdf | Write general PDF report of disease stats from R Markdown template
write_report_pdf_grouped | Write PDF grouped report from R Markdown template
write_report_xlsx | Write report Excel files